Differential Proteomics in Response to Low Temperature Diazotrophy of Himalayan Psychrophilic Nitrogen Fixing Pseudomonas migulae S10724 Strain

A novel hypothermic strain, Pseudomonas reactans WL20-3 with high nitrate removal from actual sewage, and its synergistic resistance mechanism for efficient nitrate removal at 4 °C

Nitrate can be well removed by bacteria at 25-30 °C. However, nitrate removal almost ceases at temperatures lower than 5 °C. In this study, a novel hypothermic strain, Pseudomonas reactans WL20-3 exhibited an excellent aerobic nitrate removal ability at 4 °C. It had high capability for the removal of nitrate, total dissolved nitrogen (TDN), and dissolved organic carbon (DOC) at 4 °C, achieving removal efficiencies of 100%, 87.91%, and 97.48%, respectively. The transcriptome analysis revealed all genes involved in the nitrate removal pathway were significantly up-regulated. Additionally, the up-regulation of ABC transporter genes and down-regulation of respiratory chain genes cooperated with the nitrate metabolism pathway to resist low-temperature stress. In actual sewage, inoculated with WL20-3, the nitrate removal efficiency was found to be 70.70%. Overall, these findings demonstrated the impressive capacity of the novel strain WL20-3 to remove nitrate and provided novel insights into the synergistic resistance mechanism of WL20-3 at low temperature.

Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture

Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Response of microbial communities in North Saskatchewan River to diluted bitumen and conventional crude under freeze-thaw-refreeze cycle

Microorganisms are the first responder to oil spills and their response provides insight into the ecological effects of oils on aquatic ecosystems. Limited information is available about the impact of oil spills on freshwater ecosystems under seasonal river-ice regimes. This study aimed to investigate the microbial response of North Saskatchewan River water to diluted bitumen (DB) and conventional crude (CC) during the freeze-thaw-refreeze cycle. In two separate experiments, equivalent to 2 L of fresh DB and CC were spilled on the ice-covered river water within a mesoscale spill tank. The microbial response (changes in abundance and diversity) to oils under the freeze, thaw, and refreeze cycles were assessed for 10 days using 16S rRNA gene sequencing. The results showed that microbial communities exhibited different responses to the DB and CC oils. The effect of oils was more pronounced than that of the freeze or thaw cycles. The river microbial community rapidly responded to both spills, which coincided with a steady increase in the organic content of water throughout the freeze-thaw-refreeze cycle. Microbial diversity increased after the DB spill, but remain unchanged after the CC spill, regardless of the cycles. A higher number of new taxa emerged during the ice-covered period, while more microbial enrichment (increase in abundance) was observed during the thaw cycle. Flavobacterium (37 ± 5%) and Pseudomonas (36 ± 4%) remained the most predominant genera post-DB and CC spill, respectively. The results of this study suggest that ice coverage of 5 cm did not prevent the microbial communities from the effects of oils. Thus, a quick clean-up response to an oil spill on ice-covered water is equally critical to avoid the effects of oils on the underlying freshwater ecosystems.

Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges

The Himalayas are one of the most mystical, yet least studied terrains of the world. One of Earth's greatest multifaceted and diverse montane ecosystems is also one of the thirty-four global biodiversity hotspots of the world. These are supposed to have been uplifted about 60-70 million years ago and support, distinct environments, physiography, a variety of orogeny, and great biological diversity (plants, animals, and microbes). Microbes are the pioneer colonizer of the Himalayas that are involved in various bio-geological cycles and play various significant roles. The applications of Himalayan microbiomes inhabiting in lesser to greater Himalayas have been recognized. The researchers explored the applications of indigenous microbiomes in both agricultural and environmental sectors. In agriculture, microbiomes from Himalayan regions have been suggested as better biofertilizers and biopesticides for the crops growing at low temperature and mountainous areas as they help in the alleviation of cold stress and other biotic stresses. Along with alleviation of low temperature, Himalayan microbes also have the capability to enhance plant growth by availing the soluble form of nutrients like nitrogen, phosphorus, potassium, zinc, and iron. These microbes have been recognized for producing plant growth regulators (abscisic acid, auxin, cytokinin, ethylene, and gibberellins). These microbes have been reported for bioremediating the diverse pollutants (pesticides, heavy metals, and xenobiotics) for environmental sustainability. In the current perspectives, present review provides a detailed discussion on the ecology, biodiversity, and adaptive features of the native Himalayan microbiomes in view to achieve agro-environmental sustainability.

Unraveling diverse survival strategies of microorganisms to vanadium stress in aquatic environments

Worldwide vanadium contamination is posing serious risks to ecosystems. Although abilities of microbial communities to cope with vanadium stress using specific survival strategies have been reported, little is known regarding their relative importance and the underlying detoxification/tolerance mechanisms. Herein, we investigated the potential survival strategies of microbial communities and associated pathways in aquatic environments based on geochemistry and molecular biology. High vanadium content was observed for both water (12.6 ± 1.15 mg/L) and sediment (1.18 × 10³ ± 10.4 mg/kg) in the investigated polluted stream. Co-occurrence network investigation implied that microbial communities showed cooperative interactions to adapt to the vanadium-polluted condition. Vanadium was also characterized as one of the vital factors shaping the community structure via redundancy analysis and structural equation models. Based on the metagenomic technology, three survival strategies including denitrification pathway, electron transfer, and metal resistance in innate microbes under the vanadium stress were revealed, with comprehensively summarized vanadium detoxification/tolerance genes. Remarkable role of electron transfer genes and the prevalent existence of resistance genes during detoxifying vanadium were highlighted. Overall, these findings provide novel insights into survival strategies under the vanadium contamination in aquatic environments, which can be of great significance for the identification, isolation, and application of vanadium reducing bacteria in vanadium bioremediation.

Multifarious effect of ACC deaminase and EPS producing Pseudomonas sp. and Serratia marcescens to augment drought stress tolerance and nutrient status of wheat

Drought is the prime abiotic stress that rigorously influences plant growth, yield and quality of crops. The current investigation illustrated the bio-protective characters of Serratia marcescens and Pseudomonas sp. to ameliorate drought stress tolerance, plant growth and nutrient status of wheat. The present study aimed for search of potential drought tolerant plant growth-promoting rhizobacteria (PGPR). All screened bacterial isolates exhibited potential plant growth promoting (PGP) attributes such as production of ACC deaminase, exo-polysaccharide, siderophore, ammonia, IAA, and efficiently solubilized zinc and phosphate under in vitro conditions. To assess the in situ plant growth promotion potential of PGPR, a greenhouse experiment was conducted by priming wheat seeds with screened plant PGPR. Improved water status, reactive oxygen species, osmolyte accumulation, chlorophyll and carotenoids content in plant leaves confirmed the excellent drought tolerance conferring ability of RRN II 2 and RRC I 5. Among all PGPR, RRN II 2 and RRC I 5 inoculated plants not only demonstrated greater harvest index but also exhibited more micronutrient (zinc and iron) content in wheat grains. Further, RRN II 2 and RRC I 5 were identified through 16S rDNA sequencing as S. marcescens and Pseudomonas sp., respectively. Furthermore, amplification of acdS gene (Amplified band size of acdS gene was ~ 1.8 Kb) also confirmed ACC deaminase enzyme producing ability of Pseudomonas sp. Moreover, correlation coefficient, principal component analysis and cluster analysis also demonstrated that nutrient status and values of agronomical parameters of wheat primed with S. marcescens and Pseudomonas sp. were at par with the positive control. Thus, the outcome of this comparative investigation indicates that Pseudomonas sp. and S. marcescens could be utilized as bioinoculant in wheat since they can improve the physiological status, productivity and nutrient status in wheat crop under drought.

Genome-Based Characterization of Plant-Associated Rhodococcus qingshengii RL1 Reveals Stress Tolerance and Plant-Microbe Interaction Traits

Stress tolerant, plant-associated bacteria can play an important role in maintaining a functional plant microbiome and protecting plants against various (a)biotic stresses. Members of the stress tolerant genus Rhodococcus are frequently found in the plant microbiome. Rhodococcus qingshengii RL1 was isolated from Eruca sativa and the complete genome was sequenced, annotated and analyzed using different bioinformatic tools. A special focus was laid on functional analyses of stress tolerance and interactions with plants. The genome annotation of RL1 indicated that it contains a repertoire of genes which could enable it to survive under different abiotic stress conditions for e.g., elevated mercury concentrations, to interact with plants via root colonization, to produce phytohormones and siderophores, to fix nitrogen and to interact with bacterial signaling via a LuxR-solo and quorum quenching. Based on the identified genes, functional analyses were performed in vitro with RL1 under different growth conditions. The R. qingshengii type strain djl6 and a closely related Rhodococcus erythropolis BG43 were included in the experiments to find common and distinct traits between the strains. Genome based phylogenetic analysis of 15 available and complete R. erythropolis and R. qingshengii genome sequences revealed a separation of the R. erythropolis clade in two subgroups. First one harbors only R. erythropolis strains including the R. erythropolis type strain. The second group consisted of the R. qingshengii type strain and a mix of R. qingshengii and R. erythropolis strains indicating that some strains of the second group should be considered for taxonomic re-assignment. However, BG43 was clearly identified as R. erythropolis and RL1 clearly as R. qingshengii and the strains had most tested traits in common, indicating a close functional overlap of traits between the two species.

Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency

Protein-based biomarkers can be a promising approach for identification and real-time monitoring of the bio-inoculants employed under sustainable agricultural plans. In this perspective, differential proteomics of psychrophilic diazotroph Rhodococcus qingshengii S10107 (JX173283) was performed to unravel its adaptive responses towards low-temperature nitrogen deficiency and identification of a biomarker for respective physiological conditions. LC-MS/MS-based proteome analysis mapped more than 4830 proteins including 77 up-regulated and 47 down-regulated proteins (p ≤ 0.05). Differential expression of the structural genes of nif regulon viz. nifH, nifD, and nifK along with their response regulators i.e. nifA, nifL, and nifB indicated that the nitrogenase complex was activated successfully. Besides up-regulating the biosynthesis of certain amino acids viz. Leucine, Lysine, and Alanine; the expression of the peptidoglycan synthesis proteins were also increased; while, the enzymes involved in Lipid biosynthesis were found to decrease. Furthermore, two important enzymes of the pentose phosphate pathway viz. Transketolase and Transaldolase along with Ribose import ATP-binding protein RbsA were also found to induce significantly under low temperature a nitrogen deficient condition, which suggests the cellular need for ample ribose sugar instantly. Additionally, comparative protein profiling of S10107 strain with our previous studies revealed that CowN protein was significantly up-regulated in all the cases under low-temperature nitrogen deficient conditions and therefore, can be developed as a biomarker. Conclusively, present study for the first time provides an in-depth proteome profiling of R. qingshengii S10107 and proclaims CowN as a potential protein biomarker for monitoring BNF under cold niches.

Endophytic nitrogen fixation – a possible ‘hidden’ source of nitrogen for lodgepole pine trees growing at unreclaimed gravel mining sites

Lodgepole pine (Pinus contorta var. latifolia) trees have been thriving on unreclaimed gravel mining sites in British Columbia, Canada, with tissue nitrogen-content and growth-rate unaffected by extremely low soil nitrogen-levels. This indicates that pine trees could be accessing a hidden nitrogen source to fulfill their nitrogen requirements – possibly via endophytic nitrogen-fixation. Endophytic bacteria originally isolated from native pine trees growing at gravel sites were selected (n = 14) for in vitro nitrogen-fixation assays and a year long greenhouse study to test the overall hypothesis that naturally occurring endophytic nitrogen-fixing bacteria sustain pine tree growth under nitrogen-limited conditions. Each of the 14 bacteria colonized the internal tissues of pine trees in the greenhouse study and fixed significant amounts of nitrogen from atmosphere (23%–53%) after one year as estimated through 15N isotope dilution assay. Bacterial inoculation also significantly enhanced the length (31%–64%) and biomass (100%–311%) of pine seedlings as compared to the non-inoculated control treatment. In addition, presence of the nifH gene was confirmed in all 14 bacteria. Our results support the possibility that pine trees associate with nitrogen-fixing bacteria, capable of endophytic colonization, to survive at unreclaimed gravel mining pits and this association could potentially be utilized for effective reclamation of highly disturbed sites in a sustainable manner.

Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities

With the continuous increase in the population of developing countries and decline of natural resources, there is an urgent need to qualitatively and quantitatively augment crop productivity by using new tools and technologies for improvement of agriculturally important traits. The new scientific and technological omics-based approaches have enabled us to deal with several issues and challenges faced by modern agricultural system and provided us novel opportunities for ensuring food and nutritional security. Recent developments in sequencing techniques have made available huge amount of genomic and transcriptomic data on model and cultivated crop plants including Arabidopsis thaliana, Oryza sativa, Triticum aestivum etc. The sequencing data along with other data generated through several omics platforms have significantly influenced the disciplines of crop sciences. Gene discovery and expression profiling-based technologies are offering enormous opportunities to the scientific community which can now apply marker-assisted selection technology to assess and enhance diversity in their collected germplasm, introgress essential traits from new sources and investigate genes that control key traits of crop plants. Utilization of omics science and technologies for crop productivity, protection and management has recently been receiving a lot of attention; the majority of the efforts have been put into signifying the possible applications of various omics technologies in crop plant sciences. This article highlights the background of challenges and opportunities for augmentation of crop productivity through interventions of omics technologies in India.

Quantitative proteomics of psychotrophic diazotroph in response to nitrogen deficiency and cold stress

Effective protocols and novel biomarkers are the need of this hour to screen potential cold adapted diazotrophs for sustainable mountain agricultural plans. LC-MS/MS based gel less quantitative proteomics was employed to investigate the metabolic response of Himalayan cold adapted diazotroph Pseudomonas palleroniana N26 (JN055435) for nitrogen deficiency and cold stress. More than 5000 proteins were identified, and 125 of them showed significant difference with a 2-fold or greater change (p < .05) between normal and stress conditions, including 29 up-regulated proteins and 35 down-regulated proteins. Expression of nifA, nifL, nifH, nifB, nifD, and nifK during N₂ fixing conditions reveals that nitrogenase system was successfully activated. Further, 8% of the upregulated proteins showed similarity with uncharacterized proteins of several nitrogen fixing genera which suggests their in-depth investigation. Additionally, as per earlier studies, cowN was differentially expressed under nitrogen fixing conditions; thereby, confirming its potential to be a potent biomarker for monitoring the nitrogen fixation in cold niches.

BIOLOGICAL SIGNIFICANCE

Understanding of nitrogenase expression and regulation is essential to employ potential diazotrophs under diverse ecological niches to achieve agricultural as well as environmental sustainability. The molecular mechanisms of cold adapted diazotrophy are still unaddressed. In this scenario, present study, besides characterizing diazotrophic proteins, is helpful in identifying the protein(s) or a biomarker viz. CowN to facilitate the monitoring of nitrogen fixation in cold niches. To the best of our knowledge, this is the first gel-less quantitative free-living diazotrophic proteome study using label free mass spectrometry having high mass accuracy in both MS and MS/MS scans. It enriches the diazotrophic proteome database and will complement the other "omics" technologies for improved crop protection and sustainability strategies.

MALDI mass spectrometry imaging and in situ microproteomics of Listeria monocytogenes biofilms

MALDI-TOF Mass spectrometry Imaging (MSI) is a surface-sampling technology that can determine spatial information and relative abundance of analytes directly from biological samples. Human listeriosis cases are due to the ingestion of contaminated foods with the pathogenic bacteria Listeria monocytogenes. The reduction of water availability in food workshops by decreasing the air relative humidity (RH) is one strategy to improve the control of bacterial contamination. This study aims to develop and implement an MSI approach on L. monocytogenes biofilms and proof of concept using a dehumidified stress condition. MSI allowed examining the distribution of low molecular weight proteins within the biofilms subjected to a dehumidification environment, mimicking the one present in a food workshop (10 °C, 75% RH). Furthermore, a LC-MS/MS approach was made to link the dots between MSI and protein identification. Five identified proteins were assigned to registered MSI m/z, including two cold-shock proteins and a ligase involved in cell wall biogenesis. These data demonstrate how imaging can be used to dissect the proteome of an intact bacterial biofilm giving new insights into protein expression relating to a dehumidification stress adaptation. Data are available via ProteomeXchange with identifier PXD010444.

BIOLOGICAL SIGNIFICANCE

The ready-to-eat food processing industry has the daily challenge of controlling the contamination of surfaces and machines with spoilage and pathogenic microorganisms. In some cases, it is a lost cause due to these microorganisms' capacity to withstand the cleaning treatments, like desiccation procedures. Such a case is the ubiquitous Gram-positive Bacterium Listeria monocytogenes. Its surface proteins have particular importance for the interaction with its environment, being important factors contributing to adaptation to stress conditions. There are few reproducibly techniques to obtain the surface proteins of Gram-positive cells. Here, we developed a workflow that enables the use of MALDI imaging on Gram-positive bacterium biofilms to study the impact of dehumidification on sessile cells. It will be of the most interest to test this workflow with different environmental conditions and potentially apply it to other biofilm-forming bacteria.

Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean

Nitrogen (N) is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO) using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs) were identified in the 16s rRNA and nifH libraries from nine surface samples. Of the 16s rRNA gene OTUs, 11.9% were observed in all samples while 3.5 and 15.9% were detected only in N-sufficient and N-deficient samples. Proteobacteria, Cyanobacteria and Bacteroidetes dominated the bacterial community. Prochlorococcus and Pseudoalteromonas were the most abundant at the genus level in N-deficient regimes, while SAR86, Synechococcus and SAR92 were predominant in the Kuroshio-Oyashio confluence region. The distribution of the nifH gene presented great divergence among sampling stations: Cyanobacterium_UCYN-A dominated the N-deficient stations, while clusters related to the Alpha-, Beta-, and Gamma-Proteobacteria were abundant in other stations. Temperature was the main factor that determined bacterial community structure and diversity while concentration of NO_X-N was significantly correlated with structure and distribution of N₂-fixing microorganisms. Expression of the ammonium transporter was much higher than that of urea transporter subunit A (urtA) and ferredoxin-nitrate reductase, while urtA had an increased expression in N-deficient surface water. The predicted ammonium transporter and ammonium assimilation enzymes were most abundant in surface samples while urease and nitrogenase were more abundant in the N-deficient regions. These findings underscore the fact that marine bacteria have evolved diverse N utilization strategies to adapt to different N habitats, and that urea metabolism is of vital ecological importance in N-deficient regimes.

Elucidating stress proteins in rice (Oryza sativa L.) genotype under elevated temperature: a proteomic approach to understand heat stress response

Rice is one of the widely consumed staple foods among the world's human population. Its production is adversely affected by high temperature and is more pronounced at flowering stage. Elucidating elevated temperature stress-related proteins as well as associated mechanisms is inevitable for improving heat tolerance in rice. In the present study, a proteomic analysis of heat-sensitive rice genotype, IET 21405 was conducted. Two-dimensional electrophoresis (2-DE) and MALDI-TOF/MS-based proteomics approaches revealed a total of 73 protein spots in rice leaf. The protein profiles clearly indicated variations in protein expression between the control and heat treated rice genotypes. Functional assessment of 73 expressed proteins revealed several mechanisms thought to be involved in high temperature including their putative role in metabolism, energy, protein synthesis, protein transport/storage, etc. Besides these, some proteins are expected to involve in photosynthesis, tricarboxylic acid (TCA) cycle, glycolysis and other proteins for energy production. The proteins identified in the present study provide a strong basis to elucidate gene function of these proteins and to explain further the molecular mechanisms underlying the adaptation of rice to high temperature stress.

Isolation and characterization of phosphate solubilizing bacteria from Western Indian Himalayan soils

Previous studies confirmed the existence of diversified microbial flora in the rhizosphere of Himalayan Red Kidney Bean (RKB) (Phaseolus vulgaris L.). Therefore, fifteen different temperate and subtropical regions of Western Indian Himalaya (WIH) were explored for the isolation of RKB rhizosphere-associated Phosphorus (P) solubilizing bacteria. On the basis of qPCR analysis, three soils, i.e., Munsyari, Kandakhal and Nainital soils were selected for the isolation of P solubilizers. Among 133 isolates, three bacteria viz. Lysinibaccilus macroides ST-30, Pseudomonas palleroniana N-26 and Pseudomonas jessenii MP-1 were selected based on their P solubilization potential. Moreover, in vitro seed germination assay was performed to investigate their effectiveness against four native crops viz. (Cicer arietrinum L.), (Vigna radiata L.), (Pisum sativum L.) and (Zea mays L.). Treated seeds showed significant increase in germination efficiency over their respective controls. The results suggest that Lysinibaccilus macroides ST-30, strain is a potential plant growth-promoting bacterium for chickpea (Cicer arietrinum L.) and, therefore, could be implemented as a low-cost bio-inoculant in hill agriculture system.

Cold Stress and Nitrogen Deficiency Affected Protein Expression of Psychrotrophic Dyadobacter psychrophilus B2 and Pseudomonas jessenii MP1

Nitrogen (N) deficiency and low temperature conditions are the prominent facet of Western Himalayan agro-ecosystems. A slight change in the environment alters the protein expression of the microorganisms. Therefore, proteomes of the two psychrotrophs Dyadobacter psychrophilus B2 and Pseudomonas jessenii MP1 were analyzed using two dimensional electrophoresis and MALDI–TOF–MS, to determine the physiological response of altitudinally different but indigenous microorganisms in response to cold stress under N depleting conditions. Functional assessment of 150 differentially expressed proteins from both the psychrotrophs revealed several mechanisms might be involved in cold stress adaptation, protein synthesis/modifications, energy metabolism, cell growth/maintenance, etc. In both the proteomes, abundance of the proteins related to energy production and stress were significantly increased while, proteins related to biosynthesis and energy consuming processes decreased. ATP synthase subunit alpha, beta, ATP-dependent Clp protease, Enolase, groL HtpG and N(2)-fixation sustaining protein CowN proteins were found to be expressed in both B2 and MP1, similarly to previously studied diazotrophs under low temperature N₂ fixing conditions and therefore, can be considered as a biomarker for monitoring the nitrogen fixation in cold niches. Nevertheless, in both the diazotrophs, a good fraction of the proteins were related to hypothetical proteins which are still uncharacterized, thereby, suggesting the need for in-depth studies on cold adapted diazotrophs and their adaptive mechanisms.

Diversified diazotrophs associated with the rhizosphere of Western Indian Himalayan native red kidney beans (Phaseolus vulgaris L.)

Red kidney beans (RKBs) are one of the major components in the human diet of Western Indian Himalaya (WIH). Their cultivation in these habitats is strongly influenced by various biotic and abiotic stresses and therefore, there must be a selection of RKB associated microorganisms that are adapted to these harsh conditions. Seven cold adaptive diazotrophs from the same rhizosphere were isolated in our previous study to reveal the low-temperature associated proteins and mechanisms. However, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are still unknown. In this study, RKB rhizospheric soil from two different agro-ecosystems of WIH namely S1 (Chhiplakot, 30.70°N/80.30°E) and S2 (Munsyari, 30.60°N/80.20°E) were explored for the assessment of nitrogenase reductase gene (nifH) diversity by plating respective clone libraries SN1 and SN2. The RKB rhizosphere diazotroph assemblage was very diverse and apparently consists mainly of the genera Rhizobium, followed by unknown diazotrophic microorganisms. Deduced amino acid sequence analysis revealed the presence of diverse nifH sequences, affiliated with a wide range of taxa, encompassing members of the Proteobacteria, Actinobacteria and Firmicutes. Members of cyanobacteria, methanotrophs and archaea were also detected. To the best of our knowledge, this is the first major metagenomic effort that revealed the presence of diverse nitrogen-fixing microbial assemblages in indigenous RKB rhizospheric soil which can further be explored for improved crop yield/productivity.

Differential regulation of proteins in rice (Oryza sativa L.) under iron deficiency

Sixty-three proteins were identified to be differentially accumulated due to iron deficiency in shoot and root. The importance of these proteins alterations on shoot physiology is discussed. Iron (Fe) is an essential micronutrient for plant growth and its accumulation affects the quality of edible plant organs. To investigate the adaptive mechanism of a Chinese rice variety grown under iron deficiency, proteins differentially accumulated in leaves and roots of Yangdao 6, an indica cultivar, under Fe deficiency growth condition, were profiled using a two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS). The accumulations of seventy-three proteins were detected to be increased or decreased upon iron deficiency, and sixty-three of them were successfully identified. Among the sixty-three proteins, a total of forty proteins were identified in rice leaves, and twenty-three proteins were in roots. Most of these proteins are involved in photosynthesis, C metabolism, oxidative stress, Adenosine triphosphate synthesis, cell growth or signal transduction. The results provide a comprehensive way to understand, at the level of proteins, the adaptive mechanism used by rice shoots and roots under iron deficiency.

Growth promotory potential of the cold adapted diazotroph Pseudomonas migulae S10724 against native green gram (Vigna radiata (L.) Wilczek)

It is being confirmed previously the atmospheric nitrogen fixing ability of the cold adapted Pseudomonas migulae S10724 strain at the fluctuating temperatures. Therefore, net house bioinoculation experiment was performed to determine the effectiveness of inoculation of strain S10724 on the growth enhancement of native green gram (Vigna radiata L. Wilczek). The strain significantly (p < 0.05) stimulated the growth of roots (45.3 %) and shoots (45.6 %) of green gram plants. Furthermore, other growth related parameters viz. fresh and dry weight was also found to be increased significantly. Treated plants typically showed more obvious modifications in their biochemical status also. The total chlorophyll and nitrate reductase activity was increased in S10724 inoculated plant as compared to the control one. Moreover, in vitro seed germination assay revealed that the germination was increased in S10724 strain treated seeds by 22 % at 25 °C while 25 % at 12 °C unlikely to respective controls. The results suggest that P.migulae S10724 strain is a potential plant growth promoting bacterium for legume under fluctuating temperature ranges and therefore, could be used effectively as a low cost bioinoculant in Himalayan agricultural belt successfully.